A second-grade school teacher sobbed on the witness stand in Manhattan today as she faced her alleged rapist — the drunken, off-duty cop she says brutalized her while threatening, “I’ll shoot you in the f—ing face.”

“He said, ‘You’d better come with me,'” the 25-year-old woman told jurors of the first moments of the attack, when Michael Pena approached her on an Inwood street as she headed to her first day of work at a Bronx charter school one early morning in August.

“Then he lifted his shirt and showed me his gun,” cried the woman, a petite, bespectacled brunette. She broke into tears repeatedly during her testimony, her face contorting, her soft gasps amplified over the witness stand microphone.

“I tried to offer my cell phone. My money. My wallet,” as Pena dragged her at gunpoint into an alleyway behind an apartment building, she told jurors. She remembered turning toward a distant passerby and starting to scream.

“He pulled out the gun and said, ‘Shut the f— up or I’ll shoot you.”

Again, she told jurors, she begged him to stop, pleading with him, “Please, no! No! No!”

“Then after he told me he would shoot me in the f—ing face, I didn’t say anything,” she testified.

Residents at the apartment building called 911, and Pena was caught at the scene — zipping his pants up, witnesses say. He is implicated by the DNA he left on the woman’s clothing, and after a futile, early claim that the sex was consensual, he has admitted he dragged the her to a back alley and attacked her.

But he is trying to outrun the top charges of predatory sexual assault and rape — which carry anywhere from ten years to life in prison – by claiming that he never actually managed to have intercourse with her.

“Were your knees buckling? Were you trembling? Were you scared?” defense lawyer Ephraim Savitt asked the woman repeatedly on cross examination, apparently trying to show her as too distraught during the attack to remember a detail like whether she had been physically violated.

“Petrified,” she answered. “When I realized he had a gun, yes.”

But on re-direct, prosecutor Evan Krutoy made sure the jury heard her say again, and with surety, that the statutory requirements for rape and predatory sex assault had been met.

“Is there any doubt in your mind?” Krutoy asked her, going through each of four violations charged against the drunken cop.

“No,” she answered, her voice firm.

“You felt that?” the prosecutor asked again.

“Yes,” she answered.

Pena, 28 — a three-year cop who worked out of the 33rd precinct — remains jailed in lieu of a $1 million bail bond.